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Journal Articles

Conformational dynamics of a multidomain protein by neutron scattering and computational analysis

Nakagawa, Hiroshi; Saio, Tomohide*; Nagao, Michihiro*; Inoue, Rintaro*; Sugiyama, Masaaki*; Ajito, Satoshi; Tominaga, Taiki*; Kawakita, Yukinobu

Biophysical Journal, 120(16), p.3341 - 3354, 2021/08

 Times Cited Count:1 Percentile:30.58(Biophysics)

A multi-domain protein can have various conformations in solution. Interactions with other molecules result in the stabilization of one of the conformations and change in the domain dynamics. SAXS, a well-established experimental technique, can be employed to elucidate the conformation of a multi-domain protein in solution. NSE spectroscopy is a promising technique for recording the domain dynamics in nanosecond and nanometer scale. Despite the great efforts, there are still under development. Thus, we quantitatively removed the contribution of diffusion dynamics and hydrodynamic interactions from the NSE data via incoherent scattering, revealing the differences in the domain dynamics of the three functional states of a multi-domain protein, MurD. The differences among the three states can be explained by two domain modes.

Journal Articles

Study of protein hydration via neutron scattering

Nakagawa, Hiroshi; Ajito, Satoshi

Teion Seibutsu Kogakkai-Shi, 66(2), p.83 - 92, 2021/02

Hydration and dehydration of bio-macromolecules result in the changes in the structural stabilization and biological functionality. The structure and dynamics of the hydration water are essential to understand the hydration and dehydration processes of the biosystem. Since neutron has wavelength in the order of angstrom and thermal energy, it is able to observe the structures and dynamics of the bio-molecules and hydration water. The large difference in neutron scattering cross-sections between hydrogen and deuterium provides powerful methods for emphasizing the scattering from a bio-macromolecule or hydration water by selective deuteration for hydrated biological materials. Incoherent neutron scattering and small-angle neutron scattering are able to examine the dynamics of the hydration water, and the density and structure of the hydration shell, respectively. The neutron sources, JRR-3 reactor and J-PARC accelerator, are available in Japan. The present review aims to provide the readers with brief descriptions of the neutron scattering methods and the applications to the protein hydration.

Oral presentation

Analysis of the protein hydration structure in sugar solution by quantum beam

Ajito, Satoshi

no journal, , 

Sugar is a typical bioprotectant, and is known to stabilize structures of protein. Several hypotheses have been proposed even in a simply aqueous solution system. The "hydrogen bond replacement theory" claims that protein structures are stabilized by direct hydrogen bond formation between sugar and protein. On the other hand, The "preferential hydration theory" is claims that the preferential hydration of a protein in a sugar solution put a structural change with denaturation at energetically unfavorabl. In order to structurally prove the above hypothesis, small-angle neutron scattering method and small-angle X-ray scattering method were used complementarily to analyze the hydration structure of the protein in the sugar solution. The small angle scattering method is an effective for structural analysis of biopolymers and synthetic polymers. The small-angle neutron scattering method can control the scattering density of the sample by deuteration, and is effective for multicomponent systems. In this study, the sugar was made invisible and the hydration structure of the protein was selectively observed. Analysis of the protein hydration shell using the neutron small angle scattering method revealed that the hydration shell consisting of only water was retained in the sugar solution, strongly supporting the "selective hydration theory". The result was obtained. Furthermore, as a result of investigating the dependence of "preferential hydration" on the type of sugar using X-ray, while "preferential hydration" was maintained up to about 30% for the disaccharides. For monosaccharides, penetration into the protein hydration shell was observed from around 15%. The results qualitatively explain the superior bioprotective action of disaccharides, and quantification of the above correlation is a future subject.

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